A Novato man accused of raping a woman in Sausalito was denied a reduction in bail Friday.

Ruben Flores, 43, made an initial court appearance in Marin Superior Court, where he is charged with three rape-related counts and one count of burglary. He pleaded not guilty.

His public defender, Eva Bennett, asked the judge to release Flores on his own recognizance while the case continues. Bennett described Flores, a custodian in the Kentfield School District, as a family man and 27-year Marin resident with no criminal record.

Flores' wife of 18 years was in the courtroom audience for the arraignment.

"The whole family's surprised," Bennett said.

Prosecutor Geoff Iida argued against a lower bail because of the seriousness of the allegations. Iida said the alleged victim suffered numerous bruises in the assault.

Iida also said that Flores, in an interview, acknowledged having sexual contact with the woman, but said it was consensual.

Bennett countered that Flores had known the accuser for eight years and that they'd had sexual contact in the past.

Judge James Chou left the bail as set at $100,000.

The alleged crime was reported Tuesday night when the woman, a cleaner, was working in a commercial building on Bridgeway in Sausalito. She told police that Flores, a former supervisor who had stalked her, struck her from behind and raped her while she was unconscious.

Flores is charged with forcible rape, rape of an unconscious victim, assault with intent to commit rape and burglary.

Liz Schott, superintendent of the Kentfield School District, said the district has placed Flores on administrative leave and is initiating a "personnel action" against him. She declined to specify whether the action was termination or some lesser option.

Schott said district policy allows the termination of an employee based on the nature of the allegations, regardless of whether there has been a conviction.